AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Maintain skills wiki health - check links, naming, cross-references, and coverage
インストールする前に、エージェントに与えられる指示の中身を確認できます。
The skills wiki needs regular maintenance to stay healthy: links break, skills get orphaned, naming drifts, INDEX files fall out of sync.
Core principle: Automate health checks to maintain wiki quality without burning tokens on manual inspection.
Run gardening after:
Periodic maintenance:
# Run all checks
~/.claude/garden.sh
# Or run specific checks
~/.claude/check-links.sh
~/.claude/check-naming.sh
~/.claude/check-index-coverage.sh
# Analyze search gaps (what skills are missing)
~/.claude/analyze-search-gaps.sh
The master script runs all checks and provides a health report.
check-links.sh)Checks:
@ links - backticks disable resolutionskills/ references resolve to existing filesFixes:
check-naming.sh)Checks:
Fixes:
check-index-coverage.sh)Checks:
Fixes:
❌ BROKEN: root-cause-tracing
Target: /path/to/../root-cause-tracing/SKILL.md
Fix: Update the reference path - skill might have moved or been renamed.
⚠️ ORPHANED: test-invariants/SKILL.md not in testing/INDEX.md
Fix: Add to the category INDEX:
- skills/gardening-skills-wiki/test-invariants - Description of skill
❌ BACKTICKED: condition-based-waiting on line 31
File: getting-started/SKILL.md
Fix: Remove backticks - use bare @ reference
Fix: Remove backticks:
# ❌ Bad - backticks disable link resolution
`condition-based-waiting`
# ✅ Good - bare @ reference
condition-based-waiting
❌ RELATIVE: skills/testing in coding/SKILL.md
Fix: Use skills/ absolute path instead
Fix: Convert to absolute path:
# ❌ Bad - relative paths are brittle
condition-based-waiting
# ✅ Good - absolute skills/ path
condition-based-waiting
⚠️ Mixed case: TestingPatterns (should be kebab-case)
Fix: Rename directory:
cd ~/.claude/skills/testing
mv TestingPatterns testing-patterns
# Update all references to old name
❌ NOT INDEXED: condition-based-waiting/SKILL.md
Fix: Add to testing/INDEX.md:
## Available Skills
- skills/gardening-skills-wiki/condition-based-waiting - Replace timeouts with condition polling
⚠️ EMPTY: event-based-testing
Fix: Inspect the exact directory first. Remove it only after the user explicitly confirms that the resolved path is the obsolete skill folder:
test -d ~/.claude/skills/event-based-testing && printf '%s\n' ~/.claude/skills/event-based-testing
Use the platform's native file-removal tool only after that preview and confirmation. Do not copy a broad recursive-delete command from this skill.
creating-skills, testing-skills)flatten-with-flags, test-invariants)Required fields:
name: Human-readable namedescription: One-line summarywhen_to_use: Symptoms and situations (CSO-critical)version: Semantic versionOptional fields:
languages: Applicable languagesdependencies: Required toolscontext: Special context (e.g., "AI-assisted development")# 1. Create skill
mkdir -p ~/.claude/skills/category/new-skill
vim ~/.claude/skills/category/new-skill/SKILL.md
# 2. Add to category INDEX
vim ~/.claude/skills/category/INDEX.md
# 3. Run health check
~/.claude/garden.sh
# 4. Fix any issues reported
# 1. Move/rename skills
mv ~/.claude/skills/old-category/skill ~/.claude/skills/new-category/
# 2. Update all references (grep for old paths)
grep -r "skills/gardening-skills-wiki/old-category/skill" ~/.claude/skills/
# 3. Run health check
~/.claude/garden.sh
# 4. Fix broken links
# Monthly: Run full health check
~/.claude/garden.sh
# Review and fix:
# - ❌ errors (broken links, missing skills)
# - ⚠️ warnings (naming, empty dirs)
garden.sh (Master)Runs all health checks and provides comprehensive report.
Usage:
~/.claude/garden.sh [skills_dir]
check-links.shValidates all @ references and cross-links.
Checks:
@ links (disables resolution)skills/ or skills/gardening-skills-wiki/~/) - should be skills/@ reference resolution to existing filescheck-naming.shValidates naming conventions and frontmatter.
Checks:
check-index-coverage.shValidates INDEX completeness.
Checks:
| Issue | Script | Fix |
|---|---|---|
| Backtick-wrapped links | check-links.sh | Remove backticks from @ refs |
| Relative paths | check-links.sh | Convert to skills/ absolute |
| Broken links | check-links.sh | Update @ references |
| Orphaned skills | check-links.sh | Add to INDEX |
| Naming issues | check-naming.sh | Rename directories |
| Empty dirs | check-naming.sh | Inspect the resolved directory, then remove only the confirmed empty target with the platform's native file tool |
| Missing from INDEX | check-index-coverage.sh | Add to INDEX.md |
| No description | check-index-coverage.sh | Add to INDEX entry |
Before committing skill changes:
~/.claude/garden.sh
# Fix all ❌ errors
# Consider fixing ⚠️ warnings
git add .
git commit -m "Add/update skills"
When links feel suspicious:
~/.claude/check-links.sh
When INDEX seems incomplete:
~/.claude/check-index-coverage.sh
| Excuse | Reality |
|---|---|
| "Will check links manually" | Automated check is faster and more thorough |
| "INDEX probably fine" | Orphaned skills happen - always verify |
| "Naming doesn't matter" | Consistency aids discovery and maintenance |
| "Empty dir harmless" | Clutter confuses future maintainers |
| "Can skip periodic checks" | Issues compound - regular maintenance prevents big cleanups |
Without gardening:
With gardening:
Don't manually inspect - automate the checks.
Run garden.sh after changes and periodically. Fix ❌ errors immediately, address ⚠️ warnings when convenient.
Maintained wiki = findable skills = reusable knowledge.
<!-- MCP:START --> <!-- PORTABILITY:START -->This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/gardening-skills-wiki and restart Codex after major changes.Preferred MCP Server: None required
gardening-skills-wiki outside its documented task boundary.Before claiming the gardening-skills-wiki workflow succeeded:
まだレビューはありません。使ってみた感想をお寄せください。
概要と使いどころ
AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and
日本語の概要は準備中です。原文の説明を表示しています。
12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견 반영, 답변서 점검, AI 사용 고지.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.
日本語の概要は準備中です。原文の説明を表示しています。
Multi-perspective academic paper review with dynamic reviewer personas. Runs a 5-seat, role-separated review panel (Journal-Fit Reviewer + 3 peer-review roles + Devil's Advocate) with field-specific expertise; role separation is not a claim of independent error processes. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy, 審查論文, 論文審查, 模擬審查, 同儕審查, 幫我審這篇, 以審查人角度評估, 審查者校準, 논문 심사, 동료 심사, 모의 심사, 심사자 관점에서 평가, 심사자 보정.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.
日本語の概要は準備中です。原文の説明を表示しています。